Create VAF corplots of tumors across multiple timepoints for thr autopsy samples in the PBTA Cohort

Tumor evolution project

Data used

In this notebook, we are using the maf_autopsy.tsv file generated from the 01-preprocess-data.Rmd script. We will also use the oncoprint goi list from OpenPedCan oncoprint-goi-lists-OpenPedCan-gencode-v39.csv.

Set up

suppressPackageStartupMessages({
  library(tidyverse)
  library(ggrepel)
  library(reshape2)
})

Directories and File Inputs/Outputs

# Detect the ".git" folder. This will be in the project root directory.
# Use this as the root directory to ensure proper sourcing of functions
# no matter where this is called from.
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
scratch_dir <- file.path(root_dir, "scratch")
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal") 
input_dir <- file.path(analysis_dir, "input")

# Input files
maf_autopsy_file <- file.path(scratch_dir, "maf_autopsy.tsv")
oncoprint_goi_file <- file.path(input_dir, "oncoprint-goi-lists-OpenPedCan-gencode-v39.csv")
palette_file <- file.path(root_dir, "figures", "palettes", "timepoint_color_palette.tsv")

# File path to plots directory
plots_dir <-
  file.path(analysis_dir, "plots")
if (!dir.exists(plots_dir)) {
  dir.create(plots_dir)
}

# File path to results directory
results_dir <-
  file.path(analysis_dir, "results")
if (!dir.exists(results_dir)) {
  dir.create(results_dir)
}

source(paste0(analysis_dir, "/util/function-create-corplot.R"))
source(paste0(root_dir, "/figures/scripts/theme.R"))

Read in data and process

# Read maf_autopsy file generated from step `01-process-data.Rmd`
maf_autopsy_raw <- readr::read_tsv(maf_autopsy_file, guess_max = 100000, show_col_types = FALSE) %>% 
  group_by(Kids_First_Participant_ID) %>% 
  mutate(cg_distinct = n_distinct(cancer_group) > 1) # to identify samples with different diagnosis across timepoints

# So far we have one PT_1H2REHT2 patient case with a secondary diagnosis in one of the progressive samples
# To reflect situations with multiple diagnosis, we will create `cg_sum column`
maf_autopsy <- maf_autopsy_raw %>% 
  distinct(cancer_group, .keep_all = TRUE) %>% 
  summarise(cg_sum = str_c(cancer_group, collapse = ",")) %>%
  left_join(maf_autopsy_raw, by = c("Kids_First_Participant_ID"))

# Read oncoprint_goi_file
# We will use the following list of genes and then we will create a label to select the ones for the corplots.
oncoprint_goi <- read.csv(oncoprint_goi_file, stringsAsFactor = FALSE) %>%
  select(LGAT, Embryonal.tumor, HGAT, Other) 

# let's create a list with the genes to be used for the corplots
oncoprint_goi <- data.frame(goi_list = unlist(oncoprint_goi)) 

# remove empty rows
oncoprint_goi <- oncoprint_goi[!apply(oncoprint_goi == "", 1, all), ] 
oncoprint_goi <- data.frame(oncoprint_goi)

# Read palette_df file
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE)

Corplots for each Patient case and per biospecimen_id and timepoint

# Save results by cg_sum
cg_names <- unique(as.character(maf_autopsy$cg_sum))
cg_names <- sort(cg_names, decreasing = FALSE)
print(cg_names)

[1] "Adamantinomatous Craniopharyngioma" "Atypical Teratoid Rhabdoid Tumor"  
[3] "Chordoma"                           "Diffuse midline glioma"            
[5] "Ependymoma"                         "Ewing sarcoma"                     
[7] "High-grade glioma"                  "High-grade glioma,Low-grade glioma"
[9] "Medulloblastoma"                   

# Create empty list for df
df_list <- list() 

# Loop through cg_sum
for (x in seq_along(cg_names)){
  print(x)

  cg_maf_sub <- maf_autopsy %>%
    filter(cg_sum == cg_names[x])
 
  # We will define samples based on the "Kids_First_Participant_ID" column 
  samples <- unique(as.character(cg_maf_sub$Kids_First_Participant_ID))
  print(samples)
    
  # Define cg_sum specific plots dir
  cg_plots_dir <- file.path(plots_dir, cg_names[x])
  if (!dir.exists(cg_plots_dir)) {
    dir.create(cg_plots_dir)
  }
  
  # Run loop for each sample and pair
  for (i in seq_along(samples)) {
    print(i)
    maf_sub <- cg_maf_sub %>%
      filter(Kids_First_Participant_ID == samples[i])
    timepoints_other_plots <- unique(maf_sub$timepoints_other)
    timepoints_other_plots <- timepoints_other_plots[!timepoints_other_plots == "4"]
    print(timepoints_other_plots)
    timepoints_deceased_plots <- unique(maf_sub$timepoints_deceased)
    timepoints_deceased_plots <- timepoints_deceased_plots[!timepoints_deceased_plots %in% c("1", "2", "3")]
    print(timepoints_deceased_plots)
  
    # Run corplot function
    for (t in seq_along(timepoints_deceased_plots)){
      for (k in seq_along(timepoints_other_plots)){
        
        # Plot the corplots
        fname <- paste0(cg_plots_dir, "/", samples[i], "-", timepoints_other_plots[k], "-vs-", timepoints_deceased_plots[t], "-vaf-corplot.pdf")
        print(fname)
        p <- create_corplot(maf = maf_sub,
                            timepoints_other_plot = timepoints_other_plots[k],
                            timepoints_deceased_plot = timepoints_deceased_plots[t],
                            sid = samples[i])
        pdf(file = fname, width = 10, height = 8)
        print(p)
        dev.off()
        
        
        # Print df per pair
        m <- create_corplot_melt(maf = maf_sub,
                                 timepoints_other_plot = timepoints_other_plots[k],
                                 timepoints_deceased_plot = timepoints_deceased_plots[t],
                                 sid = samples[i])
        # Assign name to df and store all df in list
        df_name <- paste(samples[i], timepoints_other_plots[k], timepoints_deceased_plots[t], sep = "-")
        df <- assign(df_name, m)
        df_list[[df_name]] <- df
       
      }
    }
  }  
}

[1] 1
[1] "PT_WYXTEG3E"
[1] 1
[1] "Progressive_BS_G9B420R9"
[1] "Deceased_BS_H13TBC1X"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Adamantinomatous Craniopharyngioma/PT_WYXTEG3E-Progressive_BS_G9B420R9-vs-Deceased_BS_H13TBC1X-vaf-corplot.pdf"

Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation ideoms with `aes()`
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "PT_3KM9W8S8" "PT_6N825561" "PT_DVXE38EX" "PT_RJ1TJ2KH"
[1] 1
[1] "Diagnosis_BS_859AV1DB"
[1] "Deceased_BS_2NQXY528" "Deceased_BS_4BB136DY" "Deceased_BS_EQQZ90JQ"
[4] "Deceased_BS_MS8TBCWJ" "Deceased_BS_P8FXRTZ2" "Deceased_BS_QR84QJN4"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_2NQXY528-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_4BB136DY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_EQQZ90JQ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_MS8TBCWJ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_P8FXRTZ2-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_QR84QJN4-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "Progressive_BS_E0S2Y0TS"
[1] "Deceased_BS_0YWFFRYV" "Deceased_BS_3V7ZNBTG" "Deceased_BS_YTCYVVY9"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_0YWFFRYV-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_3V7ZNBTG-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_YTCYVVY9-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 3
[1] "Diagnosis_BS_NSWP72M6"   "Progressive_BS_P3R9QZKP"
[3] "Recurrence_BS_Y386XSV3" 
[1] "Deceased_BS_ERRA7V0W"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Diagnosis_BS_NSWP72M6-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Progressive_BS_P3R9QZKP-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_DVXE38EX-Recurrence_BS_Y386XSV3-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 4
[1] "Diagnosis_BS_6GN1FGTB"
[1] "Deceased_BS_6VKKMM6M"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Atypical Teratoid Rhabdoid Tumor/PT_RJ1TJ2KH-Diagnosis_BS_6GN1FGTB-vs-Deceased_BS_6VKKMM6M-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 3
[1] "PT_75HRTX4S" "PT_HFQNKP5X"
[1] 1
[1] "Diagnosis_BS_7YGM7F5R"
[1] "Deceased_BS_3CDQYJ5Q" "Deceased_BS_WTGPN218"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_3CDQYJ5Q-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_WTGPN218-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "Recurrence_BS_6F49F7WH"  "Progressive_BS_9GN1QA3Q"
[3] "Progressive_BS_FBJ516WW"
[1] "Deceased_BS_2MPNPD28" "Deceased_BS_5B6XZ7YP" "Deceased_BS_FVPZ3CYY"
[4] "Deceased_BS_MAHWW7NR" "Deceased_BS_SCW1FS55" "Deceased_BS_VZB4K7NV"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Chordoma/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 4
[1] "PT_19GCSK2S" "PT_5NS35B66" "PT_FA2F3HQG" "PT_GTHZF21E" "PT_KTRJ8TFY"
[6] "PT_KZ56XHJT" "PT_MNSEJCDM" "PT_PR4YBBH3"
[1] 1
[1] "Diagnosis_BS_3KD309X6"
[1] "Deceased_BS_AH252MTC" "Deceased_BS_FZ8D57HJ" "Deceased_BS_GH6PH611"
[4] "Deceased_BS_NXT37ZPA"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_AH252MTC-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_FZ8D57HJ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_GH6PH611-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_NXT37ZPA-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "Diagnosis_BS_SVKMG97S"
[1] "Deceased_BS_F0JN3TFM"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_5NS35B66-Diagnosis_BS_SVKMG97S-vs-Deceased_BS_F0JN3TFM-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 3
[1] "Diagnosis_BS_G9WRA2N1"
[1] "Deceased_BS_S78482NX"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_FA2F3HQG-Diagnosis_BS_G9WRA2N1-vs-Deceased_BS_S78482NX-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 4
[1] "Diagnosis_BS_N4S9T8F5"
[1] "Deceased_BS_3A7YMV93" "Deceased_BS_5PR4KXE1" "Deceased_BS_D3BH8D4Y"
[4] "Deceased_BS_EV071CE1" "Deceased_BS_FQBVBTCY" "Deceased_BS_M4KR9DSE"
[7] "Deceased_BS_T3WNX1E2" "Deceased_BS_Z7806Z75"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_3A7YMV93-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_5PR4KXE1-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_D3BH8D4Y-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_EV071CE1-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_FQBVBTCY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_M4KR9DSE-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_T3WNX1E2-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_Z7806Z75-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 5
[1] "Diagnosis_BS_3VKW5988" "Diagnosis_BS_402W79TS" "Diagnosis_BS_BQ81D2BP"
[1] "Deceased_BS_5968GBGT" "Deceased_BS_AF5D41PD" "Deceased_BS_EE73VE7V"
[4] "Deceased_BS_HYKV2TH9"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 6
[1] "Progressive_BS_0ATJ22QA" "Progressive_BS_9DN4QR6E"
[3] "Diagnosis_BS_FWP8ZA4K"   "Diagnosis_BS_H8NWA41N"  
[1] "Deceased_BS_1Q524P3B" "Deceased_BS_22VCR7DF" "Deceased_BS_AK9BV52G"
[4] "Deceased_BS_D6STCMQS" "Deceased_BS_X5VN0FW0" "Deceased_BS_YHXMYDBN"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 7
[1] "Diagnosis_BS_CBMAWSAR" "Diagnosis_BS_ZSH09N84"
[1] "Deceased_BS_J8EH1N7V" "Deceased_BS_Y74XAFJX"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 8
[1] "Diagnosis_BS_PPY0EWPG"
[1] "Deceased_BS_C2NH5FDT"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Diffuse midline glioma/PT_PR4YBBH3-Diagnosis_BS_PPY0EWPG-vs-Deceased_BS_C2NH5FDT-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 5
[1] "PT_DNAJYFZT" "PT_NJQ26FHN"
[1] 1
[1] "Recurrence_BS_EJ1H9PZY"
[1] "Deceased_BS_8XJJVBQP"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_DNAJYFZT-Recurrence_BS_EJ1H9PZY-vs-Deceased_BS_8XJJVBQP-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "Recurrence_BS_JZ61AA7Z" "Diagnosis_BS_NXTB7A9N" 
[1] "Deceased_BS_7XEEQM3X" "Deceased_BS_AYR6PJN0"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ependymoma/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 6
[1] "PT_HJMP6PH2"
[1] 1
[1] "Recurrence_BS_9SVMVJ45" "Diagnosis_BS_XKM2EAT4" 
[1] "Deceased_BS_3XW15QAZ" "Deceased_BS_4CT3A9PQ" "Deceased_BS_FS48BMA3"
[4] "Deceased_BS_GXFX6VW1" "Deceased_BS_RNAADGMF"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_GXFX6VW1-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_GXFX6VW1-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_RNAADGMF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Ewing sarcoma/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_RNAADGMF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 7
[1] "PT_37B5JRP1" "PT_394ZA6P7" "PT_3CHB9PK5" "PT_8GN3TQRM" "PT_KBFM551M"
[6] "PT_MDWPRDBT" "PT_Z4BF2NSB"
[1] 1
[1] "Diagnosis_BS_EJV0N3BX"
[1] "Deceased_BS_8Q8N6AHW"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_37B5JRP1-Diagnosis_BS_EJV0N3BX-vs-Deceased_BS_8Q8N6AHW-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "Diagnosis_BS_1KP6JADZ"
[1] "Deceased_BS_Q41J76W9"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_394ZA6P7-Diagnosis_BS_1KP6JADZ-vs-Deceased_BS_Q41J76W9-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 3
[1] "Diagnosis_BS_20TBZG09"
[1] "Deceased_BS_8AY2GM4G"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_3CHB9PK5-Diagnosis_BS_20TBZG09-vs-Deceased_BS_8AY2GM4G-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 4
[1] "Recurrence_BS_QQP17PDQ"  "Progressive_BS_RXSBJ929"
[1] "Deceased_BS_S791VC80"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_8GN3TQRM-Recurrence_BS_QQP17PDQ-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_8GN3TQRM-Progressive_BS_RXSBJ929-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 5
[1] "Diagnosis_BS_9P4NDTKJ" "Diagnosis_BS_M0B42FPR" "Diagnosis_BS_M5FM63EB"
[4] "Diagnosis_BS_WYTDVC0Y"
[1] "Deceased_BS_J8EK6RNF"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_9P4NDTKJ-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_M0B42FPR-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_M5FM63EB-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_KBFM551M-Diagnosis_BS_WYTDVC0Y-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 6
[1] "Recurrence_BS_00TRPEQX"  "Recurrence_BS_BQWMQM2Y" 
[3] "Progressive_BS_D368BNRD"
[1] "Deceased_BS_1M63B97V"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Recurrence_BS_00TRPEQX-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Recurrence_BS_BQWMQM2Y-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_MDWPRDBT-Progressive_BS_D368BNRD-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 7
[1] "Recurrence_BS_EJP43CD9" "Diagnosis_BS_W2QCHQ7E" 
[1] "Deceased_BS_2T4EJ6KN" "Deceased_BS_537YFJ06" "Deceased_BS_C6T8F9K7"
[4] "Deceased_BS_GSXNQNRY" "Deceased_BS_M29BNE7Z" "Deceased_BS_MRN9VDQ0"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 8
[1] "PT_1H2REHT2"
[1] 1
[1] "Progressive_BS_79SYEHY3" "Progressive_BS_7M7JNG00"
[1] "Deceased_BS_96S0VQBN"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma,Low-grade glioma/PT_1H2REHT2-Progressive_BS_79SYEHY3-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/High-grade glioma,Low-grade glioma/PT_1H2REHT2-Progressive_BS_7M7JNG00-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 9
[1] "PT_23NZGSRJ" "PT_CXT81GRM" "PT_NZ85YSJ1"
[1] 1
[1] "Diagnosis_BS_05S9WJW6"
[1] "Deceased_BS_209RV8H2" "Deceased_BS_CCHHH752" "Deceased_BS_CJ2G78ZZ"
[4] "Deceased_BS_F2MTFYFR" "Deceased_BS_GNXGGWFN" "Deceased_BS_H8JZ6CZR"
[7] "Deceased_BS_Q03MVGN6"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_209RV8H2-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CCHHH752-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CJ2G78ZZ-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_F2MTFYFR-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_GNXGGWFN-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_H8JZ6CZR-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_Q03MVGN6-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 2
[1] "Diagnosis_BS_HZNKSQ17"
[1] "Deceased_BS_3CG2N4PD"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_CXT81GRM-Diagnosis_BS_HZNKSQ17-vs-Deceased_BS_3CG2N4PD-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

[1] 3
[1] "Diagnosis_BS_4HRYS7JY"
[1] "Deceased_BS_Q7QH96SX"
[1] "/home/rstudio/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Medulloblastoma/PT_NZ85YSJ1-Diagnosis_BS_4HRYS7JY-vs-Deceased_BS_Q7QH96SX-vaf-corplot.pdf"

Using Kids_First_Participant_ID, cg_sum, cancer_group, gene_protein, Hugo_Symbol, sym, group as id variables

# Bind all df from list and save in one file
df_list_bind <- bind_rows(df_list) %>% 
  write_tsv(file.path(results_dir, "df_list_common_genes.tsv"))

sessionInfo()

R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] ggthemes_4.2.4  reshape2_1.4.4  ggrepel_0.9.3   lubridate_1.9.2
 [5] forcats_1.0.0   stringr_1.5.0   dplyr_1.1.1     purrr_1.0.1    
 [9] readr_2.1.4     tidyr_1.3.0     tibble_3.2.1    ggplot2_3.4.0  
[13] tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0 xfun_0.38        bslib_0.4.2      colorspace_2.1-0
 [5] vctrs_0.6.2      generics_0.1.3   htmltools_0.5.5  yaml_2.3.7      
 [9] utf8_1.2.3       rlang_1.1.0      jquerylib_0.1.4  pillar_1.9.0    
[13] glue_1.6.2       withr_2.5.0      bit64_4.0.5      lifecycle_1.0.3 
[17] plyr_1.8.8       munsell_0.5.0    gtable_0.3.3     evaluate_0.20   
[21] labeling_0.4.2   knitr_1.42       tzdb_0.3.0       fastmap_1.1.1   
[25] parallel_4.2.3   fansi_1.0.4      highr_0.10       Rcpp_1.0.10     
[29] scales_1.2.1     cachem_1.0.7     vroom_1.6.1      jsonlite_1.8.4  
[33] farver_2.1.1     bit_4.0.5        hms_1.1.3        digest_0.6.31   
[37] stringi_1.7.12   rprojroot_2.0.3  cli_3.6.1        tools_4.2.3     
[41] magrittr_2.0.3   sass_0.4.5       crayon_1.5.2     pkgconfig_2.0.3 
[45] timechange_0.2.0 rmarkdown_2.21   R6_2.5.1         compiler_4.2.3